Subcellular localization of trafficking proteins in a single cell affects the assembly of trafficking machinery between organelles and vesicles throughout the targeting pathway. RabGTPase is one of the regulators to direct specific targeting of cargo molecules depending on GDP/GTP bound status. We have recently determined the crystal structures of GDP-bound inactive and both GTP- and GppNHp-bound active forms of Arabidopsis RabA1a. It is notable that the switch regions of RabA1a exhibit conformational changes derived by GDP or GTP binding. However, it was not clear that where the GDP- or GTP-bound RabA1a is localized at the subcellular level in a cell. Here we demonstrate that the distinct proportion of subcellular localization of RabA1a depends on its site-specific mutation as the GDP- or GTP-bound form. RabA1a proteins located at the plasma membrane, endosomes, and cytosol. While the GDP-bound form of RabA1a(S27N) located more at endosomes than the plasma membrane compared to the proportions of RabA1a wild-type, and the GTP-bound RabA1a(Q72L) located mainly at the plasma membrane in comparison to RabA1a wild-type and RabA1a(S27N). These distinct proportional localizations of RabA1a enable a cognate interaction between inactive/active RabA1 and effector molecules to direct specific targeting of its cargo molecules.